src/integrators/NVE.cpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
/**
 * @file NVE.cpp
 * @author tlin
 * @date 11/08/2004
 * @version 1.0
 */

#include "integrators/NVE.hpp"
#include "primitives/Molecule.hpp"
#include "utils/PhysicalConstants.hpp"

namespace OpenMD {


  NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){

  }

  void NVE::moveA(){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;
    Vector3d vel;
    Vector3d pos;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {

        vel = sd->getVel();
        pos = sd->getPos();
        frc = sd->getFrc();
        mass = sd->getMass();
                
        // velocity half step
        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;

        // position whole step
        pos += dt * vel;

        sd->setVel(vel);
        sd->setPos(pos);

        if (sd->isDirectional()){

          // get and convert the torque to body frame

          Tb = sd->lab2Body(sd->getTrq());

          // get the angular momentum, and propagate a half step

          ji = sd->getJ();

          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;

          rotAlgo_->rotate(sd, ji, dt);

          sd->setJ(ji);
        }

            
      }
    }
    flucQ_->moveA();
    rattle_->constraintA();    
  }    

  void NVE::moveB(){
    SimInfo::MoleculeIterator i;
    Molecule::IntegrableObjectIterator  j;
    Molecule* mol;
    StuntDouble* sd;
    Vector3d vel;
    Vector3d frc;
    Vector3d Tb;
    Vector3d ji;
    RealType mass;
    
    for (mol = info_->beginMolecule(i); mol != NULL; 
         mol = info_->nextMolecule(i)) {

      for (sd = mol->beginIntegrableObject(j); sd != NULL;
           sd = mol->nextIntegrableObject(j)) {

        vel = sd->getVel();
        frc = sd->getFrc();
        mass = sd->getMass();
                
        // velocity half step
        vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
                
        sd->setVel(vel);

        if (sd->isDirectional()){

          // get and convert the torque to body frame

          Tb = sd->lab2Body(sd->getTrq());

          // get the angular momentum, and propagate a half step

          ji = sd->getJ();

          ji += (dt2  * PhysicalConstants::energyConvert) * Tb;

          sd->setJ(ji);
        }

            
      }
    }
  
    flucQ_->moveB();
    rattle_->constraintB();
  }


  RealType NVE::calcConservedQuantity() {
    return thermo.getTotalEnergy();
  }

} //end namespace OpenMD
Revision:	1808
Committed:	Mon Oct 22 20:42:10 2012 UTC (12 years, 6 months ago) by gezelter
File size:	4660 byte(s)
Log Message:	A bug fix in the electric field for the new electrostatic code. Also comment fixes for Doxygen
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9	gezelter	1390	* 1. Redistributions of source code must retain the above copyright
10	gezelter	246	* notice, this list of conditions and the following disclaimer.
11			*
12	gezelter	1390	* 2. Redistributions in binary form must reproduce the above copyright
13	gezelter	246	* notice, this list of conditions and the following disclaimer in the
14			* documentation and/or other materials provided with the
15			* distribution.
16			*
17			* This software is provided "AS IS," without a warranty of any
18			* kind. All express or implied conditions, representations and
19			* warranties, including any implied warranty of merchantability,
20			* fitness for a particular purpose or non-infringement, are hereby
21			* excluded. The University of Notre Dame and its licensors shall not
22			* be liable for any damages suffered by licensee as a result of
23			* using, modifying or distributing the software or its
24			* derivatives. In no event will the University of Notre Dame or its
25			* licensors be liable for any lost revenue, profit or data, or for
26			* direct, indirect, special, consequential, incidental or punitive
27			* damages, however caused and regardless of the theory of liability,
28			* arising out of the use of or inability to use software, even if the
29			* University of Notre Dame has been advised of the possibility of
30			* such damages.
31	gezelter	1390	*
32			* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33			* research, please cite the appropriate papers when you publish your
34			* work. Good starting points are:
35			*
36			* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37			* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38			* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	246	*/
42
43	gezelter	507	/**
44			* @file NVE.cpp
45			* @author tlin
46			* @date 11/08/2004
47			* @version 1.0
48			*/
49	gezelter	246
50			#include "integrators/NVE.hpp"
51			#include "primitives/Molecule.hpp"
52	gezelter	1390	#include "utils/PhysicalConstants.hpp"
53	gezelter	246
54	gezelter	1390	namespace OpenMD {
55	gezelter	246
56
57	gezelter	507	NVE::NVE(SimInfo* info) : VelocityVerletIntegrator(info){
58	gezelter	246
59	gezelter	507	}
60	gezelter	246
61	gezelter	507	void NVE::moveA(){
62	gezelter	246	SimInfo::MoleculeIterator i;
63			Molecule::IntegrableObjectIterator j;
64			Molecule* mol;
65	gezelter	1769	StuntDouble* sd;
66	gezelter	246	Vector3d vel;
67			Vector3d pos;
68			Vector3d frc;
69			Vector3d Tb;
70			Vector3d ji;
71	tim	963	RealType mass;
72	gezelter	246
73	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
74			mol = info_->nextMolecule(i)) {
75	gezelter	246
76	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
77			sd = mol->nextIntegrableObject(j)) {
78
79			vel = sd->getVel();
80			pos = sd->getPos();
81			frc = sd->getFrc();
82			mass = sd->getMass();
83	gezelter	246
84	gezelter	507	// velocity half step
85	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
86	gezelter	246
87	gezelter	507	// position whole step
88			pos += dt * vel;
89	gezelter	246
90	gezelter	1769	sd->setVel(vel);
91			sd->setPos(pos);
92	gezelter	246
93	gezelter	1769	if (sd->isDirectional()){
94	gezelter	246
95	gezelter	507	// get and convert the torque to body frame
96	gezelter	246
97	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
98	gezelter	246
99	gezelter	507	// get the angular momentum, and propagate a half step
100	gezelter	246
101	gezelter	1769	ji = sd->getJ();
102	gezelter	246
103	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
104	gezelter	246
105	gezelter	1769	rotAlgo_->rotate(sd, ji, dt);
106	gezelter	246
107	gezelter	1769	sd->setJ(ji);
108	gezelter	507	}
109	gezelter	246
110
111	gezelter	507	}
112	gezelter	1769	}
113	gezelter	1715	flucQ_->moveA();
114			rattle_->constraintA();
115	gezelter	507	}
116	gezelter	246
117	gezelter	507	void NVE::moveB(){
118	gezelter	246	SimInfo::MoleculeIterator i;
119			Molecule::IntegrableObjectIterator j;
120			Molecule* mol;
121	gezelter	1769	StuntDouble* sd;
122	gezelter	246	Vector3d vel;
123			Vector3d frc;
124			Vector3d Tb;
125			Vector3d ji;
126	tim	963	RealType mass;
127	gezelter	246
128	gezelter	1769	for (mol = info_->beginMolecule(i); mol != NULL;
129			mol = info_->nextMolecule(i)) {
130	gezelter	246
131	gezelter	1769	for (sd = mol->beginIntegrableObject(j); sd != NULL;
132			sd = mol->nextIntegrableObject(j)) {
133
134			vel = sd->getVel();
135			frc = sd->getFrc();
136			mass = sd->getMass();
137	gezelter	246
138	gezelter	507	// velocity half step
139	gezelter	1390	vel += (dt2 /mass * PhysicalConstants::energyConvert) * frc;
140	gezelter	246
141	gezelter	1769	sd->setVel(vel);
142	gezelter	246
143	gezelter	1769	if (sd->isDirectional()){
144	gezelter	246
145	gezelter	507	// get and convert the torque to body frame
146	gezelter	246
147	gezelter	1769	Tb = sd->lab2Body(sd->getTrq());
148	gezelter	246
149	gezelter	507	// get the angular momentum, and propagate a half step
150	gezelter	246
151	gezelter	1769	ji = sd->getJ();
152	gezelter	246
153	gezelter	1390	ji += (dt2 * PhysicalConstants::energyConvert) * Tb;
154	gezelter	246
155	gezelter	1769	sd->setJ(ji);
156	gezelter	507	}
157	gezelter	246
158
159	gezelter	507	}
160	gezelter	1769	}
161	gezelter	246
162	gezelter	1715	flucQ_->moveB();
163			rattle_->constraintB();
164	gezelter	507	}
165	gezelter	246
166
167	tim	963	RealType NVE::calcConservedQuantity() {
168	gezelter	1764	return thermo.getTotalEnergy();
169	gezelter	507	}
170	gezelter	246
171	gezelter	1390	} //end namespace OpenMD